[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets BackupPortlet.java,1
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steinbeck
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From: Stefan K. <sh...@us...> - 2002-05-30 15:02:26
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets
In directory usw-pr-cvs1:/tmp/cvs-serv14855/src/java/org/openscience/nmrshiftdb/portlets
Modified Files:
BackupPortlet.java ResultPortlet.java SubmitPortlet.java
Log Message:
Changed the serialization back to JSX
Index: BackupPortlet.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/BackupPortlet.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -r1.3 -r1.4
*** BackupPortlet.java 24 May 2002 12:08:13 -0000 1.3
--- BackupPortlet.java 30 May 2002 15:02:22 -0000 1.4
***************
*** 52,58 ****
if(req.getParameter(((File)v.get(i)).getName())!=null){
numberOfRestoredFiles++;
! FileInputStream in = new FileInputStream((File)v.get(i));
! ObjectInputStream s = new ObjectInputStream(in);
! AllInOne aio=(AllInOne)s.readObject();
aio.saveMe(runData);
}
--- 52,57 ----
if(req.getParameter(((File)v.get(i)).getName())!=null){
numberOfRestoredFiles++;
! ObjIn oi=new ObjIn(new FileInputStream((File)v.get(i)));
! AllInOne aio=(AllInOne)oi.readObject();
aio.saveMe(runData);
}
Index: ResultPortlet.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/ResultPortlet.java,v
retrieving revision 1.69
retrieving revision 1.70
diff -C2 -r1.69 -r1.70
*** ResultPortlet.java 30 May 2002 09:48:55 -0000 1.69
--- ResultPortlet.java 30 May 2002 15:02:22 -0000 1.70
***************
*** 242,245 ****
--- 242,248 ----
return (new StringElement("Your input did not include a valid signal!"));
}
+ for(int i=0;i<numberSpectrum.size();i++)
+ if(((ValueTriple)numberSpectrum.get(i)).value2>1 || ((ValueTriple)numberSpectrum.get(i)).value2<0)
+ return (new StringElement("One of your intensities is more than one or less than zero. Intensities have to be between zero and one!"));
SignalComparator sigComp = new SignalComparator();
Collections.sort(numberSpectrum, sigComp);
Index: SubmitPortlet.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/SubmitPortlet.java,v
retrieving revision 1.87
retrieving revision 1.88
diff -C2 -r1.87 -r1.88
*** SubmitPortlet.java 29 May 2002 14:11:55 -0000 1.87
--- SubmitPortlet.java 30 May 2002 15:02:22 -0000 1.88
***************
*** 639,642 ****
--- 639,647 ----
bondAtoms = DBBondDBAtomPeer.doSelect(critSignals);
subData.bondAtoms=bondAtoms;
+ //And the names
+ Criteria critNames = new Criteria();
+ critNames.add(DBChemicalNamePeer.MOLECULE_ID, dbmol.getMoleculeId());
+ v=DBChemicalNamePeer.doSelect(critNames);
+ subData.chemNames=v;
}
//Add spectrum to DB
***************
*** 683,715 ****
reviewAssignment.setAssignmentDate(now);
reviewAssignment.save();
! if (nmrprops.getProperty("sendreviewmail").equals("true"))
! {
! StringBuffer url = javax.servlet.http.HttpUtils.getRequestURL(req);
! url.append("pane0/Review?nmrshiftdbaction=reviewbyurl&id=" + spectrum.getSpectrumId() + "&reviewkey=" + spectrum.getReviewKey() + "&userId="+reviewer.getPrimaryKeyAsInt());
! MailMessage email = new org.apache.turbine.util.mail.MailMessage(GeneralUtils.getSmtpServer(runData), reviewer.getEmail(), GeneralUtils.getAdminEmail(runData), "Review this input!", "Some input to NMRShiftDB has been assigned to you for review, the id is " + spectrum.getSpectrumId() + ", the URL " + url);
! if (email.send() == false)
{
! Log.error("Sending email to reviewer failed for spectrum " + spectrum.getSpectrumId());
}
! }
! //Create the overall object for serializing
! AllInOne aio=new AllInOne(dbmol, spectrum, subData.dbconditions, subData.spectrumConditions, subData.signals, subData.shifts, subData.signalAtoms, dbatoms, bondAtoms, dbbonds, chemNames);
! if (nmrprops.getProperty("writeserializedtodir").equals("true")) {
! FileOutputStream out = new FileOutputStream(nmrprops.getProperty("serializeddir")+File.separatorChar+now.toString().replace(' ','_')+"_"+time.substring(time.length()-4)+"ms"+".ser");
! ObjectOutputStream s = new ObjectOutputStream(out);
! s.writeObject(aio);
! s.flush();
! }
! if (nmrprops.getProperty("sendserializedemail").equals("true")) {
! ByteArrayOutputStream out = new ByteArrayOutputStream();
! ObjectOutputStream s = new ObjectOutputStream(out);
! s.writeObject(aio);
! s.flush();
! MailMessage email = new org.apache.turbine.util.mail.MailMessage(GeneralUtils.getSmtpServer(runData), nmrprops.getProperty("serializedemail"), GeneralUtils.getAdminEmail(runData), "Serialized input from" + now.toString(), out.toString());
! if (email.send() == false) {
! Log.error("Sending email with serialized input from " + now.toString() +" failed for spectrum " + spectrum.getSpectrumId());
}
}
-
}
catch (Exception ex)
--- 688,718 ----
reviewAssignment.setAssignmentDate(now);
reviewAssignment.save();
! try{
! if (nmrprops.getProperty("sendreviewmail").equals("true"))
{
! StringBuffer url = javax.servlet.http.HttpUtils.getRequestURL(req);
! url.append("pane0/Review?nmrshiftdbaction=reviewbyurl&id=" + spectrum.getSpectrumId() + "&reviewkey=" + spectrum.getReviewKey() + "&userId="+reviewer.getPrimaryKeyAsInt());
! MailMessage email = new org.apache.turbine.util.mail.MailMessage(GeneralUtils.getSmtpServer(runData), reviewer.getEmail(), GeneralUtils.getAdminEmail(runData), "Review this input!", "Some input to NMRShiftDB has been assigned to you for review, the id is " + spectrum.getSpectrumId() + ", the URL " + url);
! if (email.send() == false)
! {
! Log.error("Sending email to reviewer failed for spectrum " + spectrum.getSpectrumId());
! }
}
! //Create the overall object for serializing
! AllInOne aio=new AllInOne(dbmol, spectrum, subData.dbconditions, subData.spectrumConditions, subData.signals, subData.shifts, subData.signalAtoms, dbatoms, bondAtoms, dbbonds, chemNames);
! if (nmrprops.getProperty("writeserializedtodir").equals("true")) {
! FileWriter out = new FileWriter(nmrprops.getProperty("serializeddir")+File.separatorChar+now.toString().replace(' ','_')+"_"+time.substring(time.length()-4)+"ms"+".ser");
! out.write(aio.serializeMe());
! out.close();
! }
! if (nmrprops.getProperty("sendserializedemail").equals("true")) {
! MailMessage email = new org.apache.turbine.util.mail.MailMessage(GeneralUtils.getSmtpServer(runData), nmrprops.getProperty("serializedemail"), GeneralUtils.getAdminEmail(runData), "Serialized input from" + now.toString(), aio.serializeMe());
! if (email.send() == false) {
! Log.error("Sending email with serialized input from " + now.toString() +" failed for spectrum " + spectrum.getSpectrumId());
! }
}
+ }catch(Exception ex){
+ Log.error("Error when sending review mail or serializing spectrum for spectrum " + spectrum.getSpectrumId()+ ": " + ex.getMessage());
}
}
catch (Exception ex)
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